You're operating from a junior high understanding of genetics. As I pointed out earlier, coding/noncoding and sense/antisense only have meaning if applied to a particular gene. Both strands are coding for some genes and noncoding for others.
No, you are merely overstating your case by orders of magnitude.
You are taking the exception that there are some overlapping open reading frames on the anti-sense DNA strand in a number of genes and misapplying it to the problem at hand.
The fact that these O-ORF's exist does not mean that flipping the 5' to 3' orientation to allow head-to-head joining of 2 chromosomes wouldn't destroy the information on the coding strand.
The human chromosome 2 does not have the coding and anti-sense strands flipped as would be required if it were the result of 2 primate chromosomes joining head-to-head.
The problem still exists.
To say that 'both strands are coding for some genes and non-coding for others' may be 'correct' in a technical sense, but it is extremely disingenious and completely inappropriate for solving the problem at hand.
Nice try though.